Longitudinal study of Mycobacterium avium ssp. paratuberculosis fecal shedding patterns and concurrent serological patterns in naturally infected dairy cattle.

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a disease that affects ruminants worldwide. Despite global interest in the control of this disease, gaps exist in our knowledge of fecal shedding patterns and concurrent serological patterns. This longitudinal study in dairy cattle herds with high MAP seroprevalence in France aimed at accurately describing fecal shedding patterns over 1 year; relating those shedding patterns to individual animal characteristics (age, breed, parity); and exploring the association between fecal shedding patterns and serological patterns. To describe temporal fecal shedding patterns and continuity of shedding, along with the standard quantitative PCR (qPCR) threshold cycle we used a cutoff value that related to low or nonculturable fecal shedding. We also defined a threshold cycle indicative of shedding in high quantities to describe infection progression patterns. Twenty-one herds completed the study, and 782 cows were tested 4 times each. We obtained 4 sets of paired fecal qPCR and serum ELISA results from 757 cows. Although we targeted highly likely infectious animals, we found a large diversity of shedding patterns, as well as high variability between herds in the proportion of animals showing a given pattern. The fecal qPCR results of almost 20% of the final study sample were positioned at least once in the range that indicated low or nonculturable fecal shedding (between the adjusted and the standard cutoff value). Although these animals would typically be classified as non-shedders, they could be important to infection dynamics on the farm. Animals that shed at least twice consecutively and animals that shed in high quantities rarely reverted to negativity. Repeated fecal qPCR can be used to detect temporal fecal shedding traits, and the decision to cull an animal could practically be based on temporal, semiquantitative results. Overall, we found a mismatch between fecal shedding and ELISA seropositivity (637 animals were ELISA-negative 4 times, but only 13% of those animals were qPCR-negative 4 times). We found that having more than 2 ELISA-positive samples was strongly related to persistent and continuous shedding. We suggest that although serological testing is much less sensitive than qPCR, it can also be used, particularly over the course of multiple testing events, to identify animals that are most likely to contribute to the contamination of the farm environment.

A retrospective evaluation of pooled serum ELISA testing in the frame of the French eradication program for infectious bovine rhinotracheitis.

Pooled serum testing using whole-virus indirect ELISA has been recently recognized as an official method for surveillance of bovine herpesvirus 1 (BoHV1) in cattle herds in Europe. In this study, a retrospective analysis of data from the French BoHV1 surveillance campaign 2018-2019, including 7434 BoHV1-free certified herds and 157 infected herds, was performed in order to evaluate the diagnostic specificity and sensitivity of two pooled serum indirect ELISAs (from IDEXX and IDVet), in comparison with individual testing by blocking ELISAs targeting the gB and gE proteins. Pooled serum testing showed a relative specificity higher than 97.5% and a detection rate of 100% since all gB+/gE+ samples were found in positive pools. At the herd level, no more than one false positive pool was observed in most of BoHV1-free certified herds, leading to a herd relative specificity of 85.1% and 86.0% for the IDEXX and IDVet pooled serum ELISAs, respectively. Among infected herds tested by pool sizes up to 10 sera (n = 122), 46% of herds were detected through pools of size 10 containing a single positive sample, 23% through pools of size 10 containing at least two positive samples, and 31% through pools of smaller sizes. A complementary study based on manually constituted pools revealed that at least one positive sample in 100% and 93.4% of herds could be detected individually by pools of size 10 with the IDEXX and IDVet ELISAs, respectively. However, pooled serum ELISAs were influenced by the level of individual reactivity, since pools composed of either one weak-positive sample or one gB+/gE- sample could yield negative results. Altogether, these results provided the first evidence that pooled serum testing (pool size up to 10) is a suitable strategy for surveillance of BoHV1-free cattle farms.

Draft Genome Sequences of 142 Mycobacterium avium subsp. paratuberculosis Strains Isolated from Naturally Infected Dairy Cattle.

Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's disease in ruminants. Here, we report the annotated draft genome sequences of 142 M. avium subsp. paratuberculosis strains that were isolated from dairy cattle in France between 2014 and 2018. The genomes of these strains were sequenced using Illumina technology.

Virological and epidemiological patterns of swine influenza A virus infections in France: Cumulative data from the RESAVIP surveillance network, 2011-2018.

Swine influenza A viruses (swIAVs) cause acute respiratory syndromes in pigs and may also infect humans. Following the 2009 pandemic, a network was established in France to reinforce swIAV monitoring. This study reports virological and epidemiological data accumulated through passive surveillance conducted during 1,825 herd visits from 2011 to 2018. Among them, 887 (48.6 %) tested swIAV-positive. The proportion of positive cases remained stable year-on-year and year-round. The European avian-like swine H1N1 (H1avN1) virus was the most frequently identified (69.6 %), and was widespread across the country. The European human-like reassortant swine H1N2 (H1huN2) virus accounted for 22.1 % and was only identified in the north-western quarter and recently in the far north. The 2009 pandemic H1N1 (H1N1pdm) virus (3.6 %) was detected throughout the country, without settling in areas of higher pig densities. Its proportion increased in winter, during the seasonal epidemics in humans. The European human-like reassortant swine H3N2 as well as H1avN2 viruses were identified sporadically. In up to 30 % of swIAV-positive cases, pigs exhibited clinical signs of high intensity, regardless of the viral subtype and vaccination program. The recurrent pattern of the disease, i.e., an endemic infection at the herd level, was reported in 41% of cases and mainly affected post-weaning piglets (OR = 5.11 [3.36-7.76]). Interestingly, the study also revealed a significant association between the recurrent pattern and sow vaccination (OR = 1.96 [1.37-2.80]). Although restricted to the studied pig population, these results bring new knowledge about swIAV dynamics and infection patterns in pig herds in France.

Improvement of eradication program for infectious bovine rhinotracheitis in France inferred by serological monitoring of singleton reactors in certified BoHV1-free herds.

Within the framework of the national voluntary eradication program for Bovine alphaherpesvirus 1 (BoHV1) in France, the proportion of certified-free herds which experienced no more than two positive animals (termed singleton reactors) steadily increased to reach up to 95% in 2015. The aim of this study was to collate and evaluate serological data to gain insight into these epidemiological questionable BoHV1 seropositive animals. Preliminary evaluation of the performances of BoHV1 ELISA kits using a collection of 997 field sera with well-defined status revealed a relatively low specificity of the two gB blocking ELISAs most used in France for confirmatory testing (93.2% and 97.5% for gB-IDVet and gB-Idexx, respectively). In both ELISAs, the suboptimal specificity was associated with the presence of antibodies against BoHV2. Reassessment of the cut-offs led to a specificity and a sensitivity higher than 99.3%. Consequently, a comprehensive analysis of gB-positive sera from 2551 singleton reactors was performed by using gB ELISAs with optimized cut-offs, combined with viral neutralization test (campaign 2014-2015) or gE ELISA (campaign 2015-2016). Fifty percent of the 728 sera collected in 2014-2015 reacted below the optimized cut-offs in both gB ELISAs. Analysis of new blood samples collected at a minimum 6-week interval showed that these weak-positive reactions did not increase with time and could not be confirmed by confirmatory tests. Among the 1823 sera collected in 2015-2016, only 84 samples tested positive by gE ELISA, most of them corresponding to sera with reactivity above the optimized cut-offs in gB ELISAs. Screening for BoHV2 antibodies revealed a significantly increased prevalence among herds with singleton reactors, compared with the between-herd prevalence in French cattle herds. Altogether, these results provided suitable analytical strategies to limit the occurrence of false-positive BoHV1 reactions and inappropriate withdrawal of the BoHV1-free status, without alteration of diagnostic costs and reliability of eradication programs.